Recombination between poly[d(GT).d(CA)] sequences in simian virus 40-infected cultured cells

Variability of Human rDNA

In human cells, ribosomal DNA (rDNA) is arranged in ten clusters of multiple tandem repeats. Each repeat is usually described as consisting of two parts: the 13 kb long ribosomal part, containing three genes coding for 18S, 5.8S and 28S RNAs of the ribosomal particles, and the 30 kb long intergenic spacer (IGS). However, this standard scheme is, amazingly, often altered as a result of the peculiar instability of the locus, so that the sequence of each repeat and the number of the repeats in each cluster are highly variable. In the present review, we discuss the causes and types of human rDNA instability, the methods of its detection, its distribution within the locus, the ways in which it is prevented or reversed, and its biological significance. The data of the literature suggest that the variability of the rDNA is not only a potential cause of pathology, but also an important, though still poorly understood, aspect of the normal cell physiology.

Molecular characterization and a duplicated 31-bp indel within the LDB2 gene and its associations with production performance in chickens

Many studies have shown that the LDB2 gene plays a regulatory role in retinal development and the cell cycle, but its biological role remains unclear. In this study, a 31-bp indel in the LDB2 gene was found for the first time on the basis of 2797 individuals from 10 different breeds, which led to different genotypes among individuals (II, ID and DD). Among these genotypes, DD was the most dominant. Association analysis of an F₂ resource population crossed with the Gushi (GS) chicken and Anka chicken showed that the DD genotype conferred a significantly greater semi-evisceration weight (SEW, 1108.665 g ± 6.263), evisceration weight (EW, 927.455 g ± 5.424), carcass weight (CW, 1197.306 g ± 6.443), breast muscle weight (BMW, 71.05 g ± 0.574), and leg muscle weight (LMW, 100.303 g ± 0.677) than the ID genotype (SEW, 1059.079 g ± 16.86; EW, 879.459 g ± 14.446; CW, 1141.821 g ± 17.176; BMW, 67.164 g ± 1.523; and LMW, 96.163 g ± 1.823). In addition, LDB2 gene expression in different breeds was significantly higher in the breast muscles and leg muscles than in other tissues. The expression level in the breast muscle differed significantly among stages of GS chicken development, with the highest expression observed at 6 weeks. The expression levels in the pectoral muscles differed significantly among Ross 308 genotypes. In summary, we studied the relationships between a 31-bp indel in the LDB2 gene and economic traits in chickens. The indel was significantly correlated with multiple growth and carcass traits in the F₂ resource population and affected the expression of the LDB2 gene in muscle tissue. In short, our study revealed that the LDB2 gene 31-bp indel can be used as a potential genetic marker for molecular breeding.

Homologous recombination occurs frequently at innate GT microsatellites in normal somatic and germ cells in vivo

Background

In somatic cells, homologous recombination (HR) is a rare event caused by eventual DNA double-strand breaks (DSBs). In contrast, germ cells show high frequency of HR caused by programmed DSBs. Microsatellites are prone to DSBs during genome replication and, thereby, capable of promoting HR. It remains unclear whether HR occurs frequently at microsatellites both in normal somatic cells and germ cells in a similar manner.

Results

By examining the linkage pattern of multiple paternal and maternal markers flanking innate GT microsatellites, we measured HR at the GT microsatellites in various somatic cells and germ cells in a goldfish intraspecific heterozygote. During embryogenesis, the HR products accumulate gradually with the increase of the number of cell divisions. The frequency of HR at the GT microsatellites in advanced embryos, adult tissues and germ cells is surprisingly high. The type of exchanges between the homologous chromosomes is similar in normal advanced embryos and germ cells. Furthermore, a long GT microsatellite is more active than a short one in promoting HR in both somatic and germ cells.

Conclusions

HR occurs frequently at innate GT microsatellites in normal somatic cells and germ cells in a similar manner.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4758-y) contains supplementary material, which is available to authorized users.

Allelic recombination and de novo deletions in sperm in the human beta-globin gene region

Meiotic recombination is of fundamental importance in creating haplotype diversity in the human genome and has the potential to cause genomic rearrangements by ectopic recombination between repeat sequences and through other changes triggered by recombination-initiating events. However, the relationship between allelic recombination and genome instability in the human germline remains unclear. We have therefore analysed recombination and DNA instability in the delta-, beta-globin gene region and its associated recombination hotspot. Sperm typing has for the first time accurately defined the hotspot and shown it to be the most active autosomal crossover hotspot yet described, although unusually inactive in non-exchange gene conversion. The hotspot just extends into a homology block shared by the delta- and beta-globin genes, within which ectopic exchanges can generate Hb Lepore deletions. We developed a physical selection method for recovering and validating extremely rare de novo deletions in human DNA and used it to characterize the dynamics of these Hb Lepore deletions in sperm as well as other deletions not arising from ectopic exchanges between homologous DNA sequences. Surprisingly, both classes of deletion showed breakpoints that avoided the beta-globin hotspot, establishing that it possesses remarkable fidelity and does not play a significant role in triggering these DNA rearrangements. This study also provides the first direct analysis of de novo deletion in the human germline and points to a possible deletion-controlling element in the beta-globin gene separate from the crossover hotspot.

Human rDNA: Evolutionary Patterns within the Genes and Tandem Arrays Derived from Multiple Chromosomes

Human rDNA forms arrays on five chromosome pairs and is homogenized by concerted evolution through recombination and gene conversion (loci RNR1, RNR2, RNR3, RNR4, RNR5, OMIM: 180450). Homogenization is not perfect, however, so that it becomes possible to study its efficiency within genes, within arrays, and between arrays by measuring and comparing DNA sequence variation. Previous studies with randomly cloned genomic DNA fragments showed that different parts of the gene evolve at different rates but did not allow comparison of rDNA sequences derived from specific chromosomes. We have now cloned and sequenced rDNA fragments from specific acrocentric chromosomes to (1) study homogenization along the rDNA and (2) compare homogenization within chromosomes and between homologous and nonhomologous chromosomes. Our results show high homogeneity among regulatory and coding regions of rDNA on all chromosomes, a surprising homogeneity among adjacent distal non-rDNA sequences, and the existence of one to three very divergent intergenic spacer classes within each array.

Meiotic recombination hotspots: shaping the genome and insights into hypervariable minisatellite DNA change

Meiotic homologous recombination serves three principal roles. First, recombination reassorts the linkages between newly-arising alleles to provide genetic diversity upon which natural selection can act. Second, recombination is used to repair certain types of DNA damage to provide a mechanism of genomic homeostasis. Third, with few exceptions homologous recombination is required for the appropriate segregation of homologous chromosomes during meiosis. Recombination rates are elevated near DNA sites called "recombination hotspots." These sites influence the distribution of recombination along chromosomes and the timing of recombination during the life cycle. Recent advances have revealed biochemical steps of hotspot activation and have suggested that hotspots may regulate when and where recombination occurs. Two models for hotspot activation, one in which hotspots act early in the recombination pathway and one in which hotspots act late in the recombination pathway, are presented. The latter model can account for changes at hypervariable minisatellite DNA in metazoan genomes by invoking resolution of Holliday junctions at minisatellite DNA repeats.

Recombination hotspot activity of hypervariable minisatellite DNA requires minisatellite DNA binding proteins

Hypervariable minisatellite DNA repeats are found at tens of thousands of loci in the mammalian genome. These sequences stimulate homologous recombination in mammalian cells [Cell 60:95-103]. To test the hypothesis that protein-DNA interaction is required for hotspot function in vivo, we determined whether a second protein binding nearby could abolish hotspot activity. Intermolecular recombination between pairs of plasmid substrates was measured in the presence or absence of the cis-acting recombination hotspot and in the presence or absence of the second trans-acting DNA binding protein. Minisatellite DNA had hotspot activity in two cell lines, but lacked hotspot activity in two closely related cell lines expressing a site-specific helicase that bound to DNA adjacent to the hotspot. Suppression of hotspot function occurred for both replicating and non-replicating recombination substrates. These results indicate that hotspot activity in vivo requires site occupancy by minisatellite DNA binding proteins.

Identification of the transcription termination site of the mouse nkx-1.2 gene: involvement of sequence-specific factors

We have identified a transcription termination site in the 3' flanking region of the mouse nkx-1.2 gene. A downstream transcription regulatory element in the mouse nkx-1.2 gene was characterized by transferring its 3'-fragment into a chloramphenicol acetyl transferase (CAT) expression vector. Analysis of recombinant plasmids transfected into mouse NIH3T3 cells by CAT assay showed the possible region of regulation. There were two direct repeat structures containing poly(dG-dT) x poly(dC-dA) sequences (GT repeats) in this region. The precise location of transcription termination was mapped by nuclease S1 analysis of the transcripts from recombinant plasmids transfected into COSM6 cells. It was approximately 20 nucleotides upstream of the first GT repeat within the 5' sequences of the first element of the two direct repeats. Gel mobility shift assay and footprinting analysis demonstrated that nuclear DNA binding proteins bound specifically to the sequences where the termination occurred as well as the other sequences in the second element of the direct repeats. Southwestern analysis showed that 90-, 54-, 36- and 15-kDa nuclear proteins bound to the region of the termination. It is possible that one or more of those proteins are involved in blocking the elongation of the mouse nkx-1.2 gene transcript and then result in termination.

A recombination hot spot in the Rh genes revealed by analysis of unrelated donors with the rare D-- phenotype

We have studied the arrangement of Rh (rhesus) genes in donors who are completely null for the products of one of them, RHCE. We show that five of six homozygous individuals with the so-called Rh D-- phenotype, who express no red-cell antigens of the C/c and E/e series, have rearranged RHCE genes in which internal sequences have been replaced by the corresponding sequences from RHD. Moreover, although there is heterogeneity at the 3' end, the 5' boundary of this chimerism is within the same small interval around exon 2. This interval is characterized by an exceptionally high degree of sequence homology between RHCE and RHD, a high density of dispersed repetitive elements, and the presence of an alternating purine-pyrimidine copolymer tract. We suggest that these features may explain the mechanistic basis for the origin of the rearrangement.

The influence of a (GT)29 microsatellite sequence on homologous recombination in the hamster adenine phosphoribosyltransferase gene

Several DNA sequence elements are thought to stimulate homologous recombination, illegitimate recombination, or both in mammalian cells. Some are implicated by their recurrence around rearrangement breakpoints, others by their effects on recombination of extrachromosomal plasmids. None of these sequences, however, has been tested on the chromosome in a defined context. In this paper we show how the adenine phosphoribosyltransferase locus in CHO cells can be used to study the recombinogenic potential of defined DNA sequences. As an example we have measured the effect on homologous recombination of a dinucleotide repeat, (GT)29, which has been shown to stimulate homologous recombination in extrachromosomal vectors 3-20 fold. On the chromosome at the adenine phosphoribosyltransferase locus, however, this sequence shows no capacity to stimulate recombination or to influence the distribution of recombination events.

Simple repetitive sequences in the genome: structure and functional significance

The current explosion of DNA sequence information has generated increasing evidence for the claim that noncoding repetitive DNA sequences present within and around different genes could play an important role in genetic control processes, although the precise role and mechanism by which these sequences function are poorly understood. Several of the simple repetitive sequences which occur in a large number of loci throughout the human and other eukaryotic genomes satisfy the sequence criteria for forming non-B DNA structures in vitro. We have summarized some of the features of three different types of simple repeats that highlight the importance of repetitive DNA in the control of gene expression and chromatin organization. (i) (TG/CA)n repeats are widespread and conserved in many loci. These sequences are associated with nucleosomes of varying linker length and may play a role in chromatin organization. These Z-potential sequences can help absorb superhelical stress during transcription and aid in recombination. (ii) Human telomeric repeat (TTAGGG)n adopts a novel quadruplex structure and exhibits unusual chromatin organization. This unusual structural motif could explain chromosome pairing and stability. (iii) Intragenic amplification of (CTG)n/(CAG)n trinucleotide repeat, which is now known to be associated with several genetic disorders, could down-regulate gene expression in vivo. The overall implications of these findings vis-à-vis repetitive sequences in the genome are summarized.

Characterization and analysis of simple sequence repeat (SSR) loci in seashore paspalum (Paspalum vaginatum Swartz)

A size-fractionated TaqI genomic library of seashore paspalum (Paspalum vaginatum Swartz) was screened for the presence of (GA) n and (CA) n simple sequence repeats (SSRs). A total of 54 clones with a positive signal were detected among 13,000 clones screened. Forty-seven clones having repeats of n[Symbol: see text] 3 were identified, of which 85% were perfect, 13% were imperfect and 2% were compound repeat sequences. Five of ten primer pairs synthesized to amplify selected loci resulted in a product in the expected size range and were subsequently used to examine SSR polymorphisms among 46 ecotypes of P. vaginatum. The number of alleles resolved on agarose or polyacrylamide gels were similar and ranged from 6 to 16 with an average of 14 per locus. Phenetic analysis of SSR polymorphisms revealed genetic relationships among the P. vaginatum ecotypes that were in general agreement with relationships determined previously by RAPD analysis of the same plant materials. Further screening of the genomic library did not identify (AT) n , trimeric or tetrameric repeats. Hybridization of an (ATT)8 oligonucleotide probe to genomic DNA isolated from I. batatas, E. coli, Citrullis lanatus and P. vaginatum suggested that the P. vaginatum genome contained significantly fewer ATT repeats than either the I. batatas or C. lanatus genome.

Identification of a liver-specific promoter for the ovine growth hormone receptor

Growth hormone (GH) receptor cDNA clones from several species are characterized by heterogeneity in the 5' untranslated region (5'UT). This has been attributed to different promoters directing the expression of the gene from exons encoding 5'UT's which are alternatively spliced onto a common splice acceptor 11 basepairs (bp) upstream of the initiating AUG on exon 2. The following study identifies exon 1A of the ovine (o) GH receptor gene, corresponding to the 5'UT of a developmentally regulated, liver-specific transcript. Exon 1A spans 206 bp at a position 17 kilobases (kb) upstream of exon 2. Sequencing of the 669 bp region 5' to the transcription initiation site (+1) reveals a TATA box at -31, a CCAAT box at -88, and putative binding sites for several transcription factors involved in liver-specific gene expression. Two repetitive sequence elements are located in the 5' and 3' flanking regions of exon 1A. Functional analysis of the 4.5 kb region upstream of exon 1A was performed by transfecting the human hepatoma cell line HuH7 with luciferase reporter gene constructs. Positive and negative regulatory regions are identified, with basal promoter activity within 473 bp of the transcription initiation site. A 47 bp region containing putative binding sites for the activated glucocorticoid receptor and C/EBP-like proteins, between -180 and -133, is essential for transcriptional activation.

Z-DNA-forming sequences at a putative duplication site in the human annexin VI-encoding gene

We report here the presence of five stretches of alternating purine/pyrimidine (APP) intronic sequence close to the 5' end of the first exon in the C-terminal half of the human annexin VI-encoding gene (ANX VI). ANX VI, which comprises eight conserved repeats, is considered to have arisen by duplication of a hypothetical four repeat Anx; the location of the duplication would be predicted to occur within the intron where the APP sequences have been identified. The APP sequences have, by computer prediction, been identified as having significant potential to form Z-DNA. We discuss the significance of these potential Z-DNA-forming sequences being located in a region predicted to be the site of duplication which gave rise to the human ANX VI gene.

The Q300 gene: a novel transcription unit induced in simian virus 40-infected and -transformed mouse cells

The Q300 element is a single-copy 233-bp genomic mouse DNA fragment carrying a high-affinity binding site for the simian virus 40 (SV40) large T antigen. This element was used to screen an EMBL3 mouse genomic library. We could identify a genomic clone containing an approximately 500-bp transcribed region flanking the Q300 element. The transcribed region, termed the Q300 transcription unit or Q300 gene, is overexpressed in acutely SV40-infected or SV40-transformed mouse and rat cells. The Q300 gene includes an open reading frame which has the coding potential for a small polypeptide with an extremely hydrophobic N terminus and a hydrophilic C terminus. The deduced polypeptide has some similarity with the papillomavirus E5 oncoprotein.

AT repeats in barely genome

The DNA sequence (AT)26 of barley genome has been cloned. This sequence is arranged in intraspecific locus and is repeated 1500 times per haploid genome. This fragment is not translated and can form cruciform structures in the AT region.

Allelic variations of human TCR V gene products

A central problem confronting the immune system is how to discriminate among vast numbers of antigens. Novel genetic ploys that aid the discriminative process, including complex gene rearrangements (in antibody and T-cell receptor (TCR) genes) and extensive allelic polymorphism (in major histocompatibility complex (MHC) genes), have been described. Recent evidence has suggested a further level of diversity; TCR V gene allelic variation. In this article David Posnett summarizes evidence in favour of this possibility and speculates on the possible functional consequences of TCR allelism.

Vertebrate protamine gene evolution I. Sequence alignments and gene structure

The availability of the amino acid sequence for nine different mammalian P1 family protamines and the revised amino acid sequence of the chicken protamine galline (Oliva and Dixon 1989) reveals a much close relationship between mammalian and avian protamines than was previously thought (Nakano et al. 1976). Dot matrix analysis of all protamine genes for which genomic DNA or cDNA sequence is available reveals both marked sequence similarities in the mammalian protamine gene family and internal repeated sequences in the chicken protamine gene. The detailed alignments of the cis-acting regulatory DNA sequences shows several consensus sequence patterns, particularly the conservation of a cAMP response element (CRE) in all the protamine genes and of the regions flanking the TATA box, CAP site, N-terminal coding region, and polyadenylation signal. In addition we have found a high frequency of the CA dinucleotide immediately adjacent to the CRE element of both the protamine genes and the testis transition proteins, a feature not present in other genes, which suggests the existence of an extended CRE motif involved in the coordinate expression of protamine and transition protein genes during spermatogenesis. Overall these findings suggest the existence of an avian-mammalian P1 protamine gene line and are discussed in the context of different hypotheses for protamine gene evolution and regulation.

Hypervariable minisatellite DNA is a hotspot for homologous recombination in human cells

Hypervariable minisatellite DNA sequences are short tandemly repeated sequences that are present throughout the human genome and are implicated to enhance recombination. We have constructed a consensus hypervariable minisatellite sequence and analyzed its effect on homologous recombination in human cells in culture. The consensus sequence d(AGAGGTGGGCAGGTGG)6.5 is shown to stimulate homologous recombination up to 13.5-fold. The stimulation occurs at a distance and in both directions but does show a quantitative directionality. Stimulation occurs in a codominant manner, and the sequence is inherited equally in the products. Enhancement is maintained, but at a reduced level, when double-strand breaks are introduced into the substrates. Multiple unselected recombination events are promoted, and preferential stimulation of reciprocal exchange events is demonstrated.

Hyperreactivity of B-Z junctions to 4,5',8-trimethylpsoralen photobinding assayed by an exonuclease III/photoreversal mapping procedure

We have developed an exonuclease III/photoreversal procedure to map, with base-pair resolution, the bases that have photoreacted with 4,5',8-trimethylpsoralen (Me3-psoralen) forming either monoadducts or interstrand crosslinks in DNA. This assay allows quantification of relative rates of Me3-psoralen photobinding to bases in DNA at levels less than one crosslink per 8000 base-pairs. We demonstrate the applicability of the Me3-psoralen mapping procedure on the Z-forming sequence GAATT(CG)6-TA(CG)6AATTC. The results confirm our previous findings that Me3-psoralen forms crosslinks in the 5'TA within the (CG)6TA(CG)6 sequence when it exists in the B conformation but not when it exists in the Z conformation. In addition, with increasing superhelical density we observe at least a hundred-fold increased Me3-psoralen presumably represent B-Z junctions. The two presumed junctions respond differently with increasing negative superhelical tension, however, suggesting that the structures of these negative superhelical tension, however, suggesting that the structures of these junctions differ. This increased Me3-psoralen photoreactivity provides a positive signal for the presence of Z-DNA. The sequence and assay described here provide a "torsionally tuned probe" for determining the effective superhelical density of DNA in vivo.

Structural analysis of a rat renal kallikrein gene

A renal kallikrein gene has been isolated, sequenced and characterized from a rat genomic library using a kallikrein cDNA probe. The kallikrein gene is 4160 bases in length and consists of 5 exons and 4 introns. The deduced sequence of the gene encodes an 18 amino acid (a.a.) signal peptide, a 6 a.a. propeptide and a 237 a.a. active enzyme with an N-terminal valine. A sequence comparison of this and tissue kallikrein (pancreatic kallikrein) indicates the key a.a. residues for serine protease activity (HIS-ASP-SER) and cleavage specificity at basic a.a. Northern blot analysis using a specific oligonucleotide probe reveals that this gene is expressed specifically in the kidney but not in the pancreas. This gene is also expressed non-specifically in the submandibular gland which expresses all kallikrein family genes. The expression of this kidney-specific kallikrein gene is regulated by steroid hormones.

Molecular cloning and characterization of two rat renal kallikrein genes

Kallikreins compose a multigene family coding for a subgroup of serine proteases, which are involved in the processing of bioactive peptides. Two rat kallikrein-related genes, RSKG-7 (rat submandibular gland kallikrein gene 7) and RSKG-3, have been cloned and their sequences analyzed. RSKG-7 is approximately 4200 bases in length and consists of five exons and four introns. The 5' end region contains the variant CATAT box and TTTAAA box; the 3' end region contains the polyadenylation signal AATAAA. This gene encodes a putative 28,935-dalton preproenzyme of 261 amino acids (aa). The active enzyme consists of 237 aa and is preceded by a deduced signal peptide of 18 aa and a profragment of 6 aa. RSKG-3 is highly homologous to RSKG-7 in terms of its sequence and structure; it encodes a 28,730-dalton prepropeptide consisting of a signal peptide of 18 aa, a profragment of 6 aa, and an active peptide of 235 aa. Sequence comparisons of RSKG-7, RSKG-3, and other kallikrein-related enzymes reveal the key amino acid residues needed for both serine protease activity (His/Asp/Ser) and kallikrein-like cleavage specificity at basic amino acids. Northern blot analyses using specific oligonucleotide probes demonstrate that, among the 12 tissues studied, RSKG-7 and RSKG-3 are expressed in the rat kidney and submandibular gland. Castration of male rats results in a decrease in submandibular gland RSKG-7 mRNA, which can be restored to the normal level by treatment with thyroxine or testosterone. On the other hand, neither castration nor hormonal manipulation affects RSKG-7 mRNA levels in the kidney.

A rapidly evolving region in the immunoglobulin heavy chain loci of rat and mouse: postulated role of (dC-dA)n.(dG-dT)n sequences

The nucleotide sequences of the introns that are located between the C4 exon and the first membrane exon of mouse and rat immunoglobulin epsilon-chain genes have been determined. The rat intron sequence was found to contain four separate clusters of repetitive sequences all of which consisted of (dC-dA)n.(dG-dT)n dinucleotide repeats. A comparison between this chromosomal region in mouse and rat revealed four deletions or duplications, three of which have occurred inside or at the borders of the CA clusters. Rearrangements have occurred inside or at the borders of all four repeats after the evolutionary separation of mouse and rat. The sequence comparison reveals in addition a duplication, connected to the CA repeats, which has occurred early in evolution, before the evolutionary divergence of mouse and rat. These findings suggest that (dC-dA)n.(dG-dT)n sequences are potential targets for recombination events.

Integration of cellular-SV40 DNA and the thermal stability of the recombinant sites. Brief report

We calculated the predicted melting profiles of evolutionary variants of SV40 and compared the nucleotide sequences of large T antigen binding sites and recombinant sites for homology. Neither is critically important in selecting a recombinant site for SV40-SV40 and SV40-cellular DNA fragments.

Simple repetitive sequences in the genomes of archaebacteria

Stretches of simple sequences poly(dG-dT).poly(dC-dA), poly(dG-dA).poly(dC-dT), poly(dG).poly(dC) and poly(dA).poly(dT), the occurrence of which is a characteristic feature of eukaryotic genomes, are found in the genomes of archaebacteria Halobacterium halobium and Sulfolobus acidocaldarius. In S. acidocaldarius these sequences constitute a considerable portion of the genome; they belong to a class of repetitive sequences dispersed throughout the genome, being transcribed and found in RNAs of different lengths.

SV40-based Escherichia coli shuttle vectors infectious for monkey cells

We describe SV40-based Escherichia coli shuttle vectors which can be packaged as pseudovirions without excision of plasmid sequences and which can be rescued in bacteria. These vectors replicate and are transmitted as virus in monkey COS cells without requiring a helper virus. Extrachromosomal vector DNA isolated from infected cells can be rescued in E. coli, so that DNA alterations can be easily screened. Indeed, some of the constructions give rise to very stable plasmids with no detectable rearrangements after multiple lytic cycles in COS cells. The spontaneous mutation frequency measured in bacteria, on the lacO target, is smaller than those usually found with shuttle vectors. We also constructed an expression vector derived from one of our infectious viruses by inserting the chloramphenicol acetyl transferase gene, expressed from the SV40 early promoter, which is efficiently transduced to cells by infection. In this system, the shuttle virus combines the convenience of plasmid rescue and analysis in bacteria, with the advantages of infectious virus.

Homologous pairing of DNA molecules by Ustilago rec1 protein is promoted by sequences of Z-DNA

Plasmids containing Z-DNA stretches can be paired and linked by combined action of Ustilago rec1 protein and topoisomerase. The product formed is a hemicatenated dimer in which two DNA rings are topologically intertwined at a region of homology. Superhelicity governs the reaction. Formation of linked product is coupled with formation of Z-DNA in the plasmid, a process dependent on the superhelix density. Pairing appears to initiate within the Z-DNA sequence, not at the unwound B-Z junction. The reaction can be blocked by a Z-DNA-specific binding protein, namely Z-DNA antibody. Plasmids with alternating Z-DNA dG-dC sequences at different sites on otherwise homologous molecules can be linked at the dG-dC sequences. However, a plasmid with a (dG-dC)n.(dG-dC)n Z-DNA stretch cannot be linked with a plasmid containing a (dG-dT)n.(dC-dA)n Z-DNA stretch.

Analysis of homologous recombination in cultured mammalian cells in transient expression and stable transformation assays

Recombination between plasmid molecules, each containing a nonoverlapping deletion mutation in the hamster adenine phosphoribosyltransferase gene, was measured after coinjection into rat cells. Using these two plasmids, as linear or circular molecules, the recombination efficiency was measured soon after injection in a transient expression assay or after selection for stable transformants. The transient assay revealed that linear molecules were a better substrate for recombination, with double strand breaks within the region of homology stimulating recombination more than breaks outside the region of homology. A 20 to 70-fold increase in the efficiency of recombination was observed when two linear molecules were coinjected as compared to two circular molecules. Linear molecules were found to not only stimulate recombination but also to facilitate stable integration of the recombinant molecule into the host genome.